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PubMed1992

Theoretical study of near neutrality. II. Effect of subdivided population structure with local extinction and recolonization.

There are several unsolved problems concerning the model of nearly neutral mutations. One is the interaction of subdivided population structure and weak selection that spatially fluctuates. The model of nearly neutral mutations whose selection coefficient spatially fluctuates has been studied by adopting the island model with periodic extinction-recolonization. Both the number of colonies and the migration rate play significant roles in determining mutants' behavior, and selection is ineffective when the extinction-recolonization is frequent with low migration rate. In summary, the number of mutant substitutions decreases and the polymorphism increases by increasing the total population size, and/or decreasing the extinction-recolonization rate. However, by increasing the total size of the population, the mutant substitution rate does not become as low when compared with that in panmictic populations, because of the extinction-recolonization, especially when the migration rate is limited. It is also found that the model satisfactorily explains the contrasting patterns of molecular polymorphisms observed in sibling species of Drosophila, including heterozygosity, proportion of polymorphism and fixation index.

Animals↗
PubMed2006

Population structure within and between subspecies of the Mediterranean triplefin fish Tripterygion delaisi revealed by highly polymorphic microsatellite loci.

Although F(ST) values are widely used to elucidate population relationships, in some cases, when employing highly polymorphic loci, they should be regarded with caution, particularly when subspecies are under consideration. Tripterygion delaisi presents two subspecies that were investigated here, using 10 microsatellite loci. A Bayesian approach allowed us to clearly identify both subspecies as two different evolutionary significant units. However, low F(ST) values were found between subspecies as a consequence of the large number of alleles per locus, while homoplasy could be disregarded as indicated by the standardized genetic distance G'(ST). Heterozygosity saturation was observed in highly polymorphic loci containing more than 15 alleles, and this threshold was used to define two loci pools. The less variable loci pool revealed higher genetic variance between subspecies, while the more variable pool showed higher genetic variance between populations. Furthermore, higher differentiation was also observed between populations using G'(ST) with the more variable loci. Nonetheless, a more reliable population structure within subspecies was obtained when all loci were included in the analyses. In T. d. xanthosoma, isolation by distance was detected between the eight analysed populations, and six genetically homogeneous clusters were inferred by Bayesian analyses that are in accordance with F(ST) values. The neighbourhood-size method also indicated rather small dispersal capabilities. In conclusion, in fish with limited adult and larval dispersal capabilities, continuous rocky habitat seems to allow contact between populations and prevent genetic differentiation, while large discontinuities of sand or deep-water channels seems to reduce gene flow.

Alleles↗
PubMed2000

Microsatellite size homoplasy, SSCP, and population structure: a case study in the freshwater snail Bulinus truncatus.

The extent of microsatellite size homoplasy, as well as its effect on several population genetics statistics, was investigated in natural populations using the single-strand conformation polymorphism (SSCP) method. The analysis was conducted using 240 individuals from 13 populations of the freshwater snail Bulinus truncatus at a GT(n)CT(m) compound microsatellite locus. We showed that SSCP can be used to uncover, at least partly, size homoplasy in the core sequence of this category of loci. Eight conformers (SSCP variants) were detected among the three size variants (electromorphs). Sequencing revealed that each conformer corresponded to a different combination of repeats in the GT(n) and CT(m) arrays. Part of this additional variability was detected within populations, resulting in a substantial increase in gene diversity in four populations. Additional variability also changed the values of parameters used to analyze population differentiation among populations: pairwise tests of differentiation were significant much more often with conformers than with electromorphs. On the other hand, pairwise estimates of F(st) were either smaller or larger with conformers than with electromorphs, depending on whether or not electromorphs were shared among populations. However, estimates of F(st) (or analogs) over all populations were very similar, ranging between 0.66 and 0.75. Our results were consistent with the theoretical prediction that homoplasy should not always lead to stronger population structure. Finally, conformer sequences and electromorph size distribution suggested that single-point and/or stepwise mutations occurring simultaneously in the different repeated arrays of compound microsatellites produce sequence variation without size variation and hence generate more size homoplasy than expected under a simple stepwise mutation model.

Animals↗
PubMed1994

Variation in mitochondrial DNA and population structure of the Taipei treefrog Rhacophorus taipeianus in Taiwan.

Mitochondrial DNA (mtDNA) from 40 samples of the Taipei treefrog Rhacophorus taipeianus collected from seven populations in Taiwan were sequenced to document the DNA sequence variation in anuran mtDNA and to elucidate the phylogeographic population structure in the Taipei treefrog. Sequences of 722-764 bases in length, including a 108-bp segment of the cytochrome b gene and a 614-656-bp D-loop segment, were obtained by direct sequencing using polymerase chain reaction (PCR). The variation in length was due to a 40-bp region that tandemly repeated four to five times in the D-loop region. The first repeat is the most conserved one among the five repeats because there are no variable sites in this repeat. Besides the 40-bp length variation, 28 positions in the 764-bp sequences are variable and distributed evenly in the cytochrome b gene fragment and D-loop region. Variation in the D-loop of the Taipei treefrog is comparable to those of other vertebrates. Two well-differentiated lineages (northern and central) differing by mean sequence divergence of 1.7% are identified and concordant with their geographic distributions. The two lineages are inferred to have split from a common ancestral population in the early Pleistocene. However, the interpopulation divergence of the northern lineage (< 0.33%) is apparently lower than that of the central lineage (1.11%), implying that the two lineages evolved independently and had different demographic histories after divergence. This study reveals that anuran D-loop has potential as a genetic marker in phylogenetic and population genetic analyses of anurans.

Animals↗
PubMed2004

Population structure of loggerhead shrikes in the California Channel Islands.

The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.

Animals↗
PubMed1998

Population structure and gene flow of the Atlantic walrus (Odobenus rosmarus rosmarus) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation.

The population structure of the Atlantic walrus, Odobenus rosmarus rosmarus, was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH-dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from northwest (NW) Greenland, east (E) Greenland, Svalbard and Franz Joseph Land. Two of the 10 haplotypes detected in the four samples were diagnostic for the NW Greenland sample, which implied that the group of walruses in this area is evolutionary distinct from walruses in the other three areas. One individual sampled in E Greenland exhibited a Pacific haplotype, which proved a connection between the Pacific walrus and walruses in eastern Greenland. The Franz Joseph Land, Svalbard and E Greenland samples shared the most common haplotype, indicating very little differentiation at the mtDNA level. Gene flow (Nm) estimates among the four areas indicated a very restricted exchange of female genes between NW Greenland and the more eastern Atlantic Arctic samples, and a closer relationship between the three samples composing the eastern Atlantic Arctic. The genetic variation at 11 polymorphic microsatellite loci grouped individuals into three populations, NW Greenland, E Greenland and a common Franz Joseph Land-Svalbard population, which were connected by moderate gene flow.

Animals↗
PubMed1990

Population structure of the Peljesac Peninsula, Yugoslavia.

We gathered serogenetic and parent-offspring migration data from 604 residents of 7 villages on the Peljesac peninsula in southern Yugoslavia. A variety of population genetics and multivariate statistics models and procedures give a concordant picture of the population structure of this region. Extensive migration is the dominant microevolutionary force patterning the variation seen today. Multiple population bottlenecks have also occurred over the past few centuries as a result of disease, famine, war, economic failure, and founder events, making it likely that genetic drift has been an important factor in the history of this population system.

Adult↗
PubMed1991

Effects of population structure on DNA fingerprint analysis in forensic science.

DNA fingerprints are used in forensic sciences to identify individuals. However, current analyses could underestimate the probability of two individuals sharing the same profile because the effect of population structure is not incorporated. An alternative analysis is proposed to take into account population stratification. The analysis uses studies of inbreeding in human populations to obtain an empirical upper bound on the magnitude of the effect.

Alleles↗
PubMed1995

Population structure, fitness surfaces, and linkage in the shifting balance process.

Wright first introduced the idea that random genetic drift and classical mass-action selection might combine in such a way as to allow populations to find the highest peak in complicated adaptive surfaces. His theory assumes large but structured populations, in which mating is spatially local. If gene flow is sufficiently low, and the subpopulations (demes) are small enough, they will be subject to genetic drift. Distant demes drift independently, allowing many independent searches of the adaptive surface to take place. A deme that has shifted to a higher peak can, by emigration, cause the rest of the demes to shift to the higher peak. The probability of this shift depends on the migration rate. Previous studies have concluded that very little migration is necessary to effect the shift in adaptive peaks that characterizes the last phase of Wright's Shifting Balance Process (SBP). Here we present the results of a computer study that investigates the roles of dispersal distance, the degree of epistasis in the fitness surface, and recombination on the shifting balance process. In particular, we measure their effect on the population's mean fitness. We show that over a range of dispersal distances the advantage of the SBP is a monotonically increasing function of the amount of epistasis. Our results show that the extent of dispersal that results in the greatest effect of the SBP in increasing mean fitness depends on the extent of epistasis. Finally, for low levels of epistasis, higher recombination performs better, while for intermediate levels, lower recombination results in a greater advantage of the SBP.

Adaptation, Biological↗
PubMed2006

[Genetic diversity and population structure of BMY and brahman cattle revealed by six microsatellite loci].

The genetic variations and polymorphisms of six microsatellite loci were analyzed to determine the population structure and breeding progress of BMY and Brahman cattle. The range of polymorphic information content of six loci was 0.524-0.752. The unbiased expected and observed heterozygosity were similar and were 0.7376 and 0.7396, 0.6412 and 0.6537 for BMY and Brahman cattle, respectively. The expected heterozygosity was relatively high in the second generation of BMY in inter se breeding, which was congruent with the breeding progress. In addition, the value for Red Angus was 0.4609, which was lower and close to the Japanese Brown cattle (0.471), and may indicate its relative homogeneity.

Animals↗
PubMed2001

Invasion history and genetic population structure of riverine macroinvertebrates.

Macroinvertebrate communities of large rivers have experienced dramatic species turnovers in the last decades, which still go on. The analysis of genetic population structure plays a central role in understanding and predicting these biological invasions. Two points of view are considered: the influence of the invasion history on the genetic structuring and the potential implications of genetic structure for future invasibility. Expectations about selectively neutral genetic variation in simple invasion models are compared to case studies of amphipods and Dreissena. The genetic patterns of one amphipod species of the Gammarus fossarum complex yield strong evidence for a stepwise regional colonisation. Other invasive amphipods show similar, but less clear genetic characteristics. Long-distance colonisation is probably common in Dreissena polymorpha, but subsequent downstream swamping of larvae obscures the expected genetic pattern by homogenising neighbouring populations. First, a brief review of general characteristics of riverine invasions is followed by a discussion of the utility of genetic tools for inferring taxon and source population identity.

Journal Article↗
PubMed1989

Characterization of the bacterial population structure in an anaerobic-aerobic activated sludge system on the basis of respiratory quinone profiles.

Bacterial respiratory quinones were used as biomarkers for studying the bacterial population structure, especially the content of Acinetobacter species, in a laboratory-scale anaerobic-aerobic activated sludge system and in the standard aerobic system. All tested sludges contained both ubiquinone and menaquinone, with a molar ratio of about 1:0.5. High-performance liquid chromatography showed that ubiquinone with eight isoprene units (Q-8) was present as the predominant ubiquinone, Q-10 was the second most common type, and Q-9 and other homologs were minor components in the anaerobic-aerobic sludge and the standard aerobic sludge. Bacteriological examination indicated that, in both sludge systems, Q-8-containing bacteria constituted a large proportion of the aerobic heterotrophic bacterial flora, but only a few strains with Q-9 were found. These findings demonstrate that the population of Acinetobacter species, which contain Q-9 as the major quinone, is negligible in those environments. The present results suggest that the introduction of anaerobic conditions into the aerobic batch process has little influence on the bacterial community structure.

Aerobiosis↗
PubMed1981

Population structure of Alaskan and Siberian indigenous communities.

Genetic data consisting of 14 red cell antigen groups and 11 serum and erythrocytic protein marker systems from four Eskimo populations of the Norton Sound area of Alaska are reported. The population structure of these four groups in analyzed both separately and within the larger context by comparison to 15 other circumpolar groups. These analyses reveal a good fit between genetic structure, geographic distribution, linguistic affiliation, and the ethnohistory of the region.

Alaska↗
PubMed2000

Consistency and fluctuation theorems for discrete time structured population models having demographic stochasticity.

In this paper we prove a consistency theorem (law of large numbers) and a fluctuation theorem (central limit theorem) for structured population processes. The basic assumptions for these theorems are that the individuals have no statistically distinguishing features beyond their class and that the interaction between any two individuals is not too high. We apply these results to density dependent models of Leslie type and to a model for flour beetle dynamics.

Animals↗
PubMed1992

Assessment of genetic diversity and population structure of Xanthomonas oryzae pv. oryzae with a repetitive DNA element.

A repetitive DNA element cloned from Xanthomonas oryzae pv. oryzae was used to assess the population structure and genetic diversity of 98 strains of X. oryzae pv. oryzae collected between 1972 and 1988 from the Philippine Islands. Genomic DNA from X. oryzae pv. oryzae was digested with EcoRI and analyzed for restriction fragment length polymorphisms (RFLPs) with repetitive DNA element as a probe. Twenty-seven RFLP types were identified; there was no overlap of RFLP types among the six races from the Philippines. Most variability (20 RFLP types) was found in strains of races 1, 2, and 3, which were isolated from tropical lowland areas. Four RFLP types (all race 5) were found among strains isolated from cultivars grown in the temperate highlands. The genetic diversity of the total population of X. oryzae pv. oryzae was 0.93, of which 42% was due to genetic differentiation between races. The genetic diversities of strains collected in 1972 to 1976, 1977 to 1981, and 1982 to 1986, were 0.89, 0.90, and 0.92, respectively, suggesting a consistently high level of variability in the pathogen population over the past 15 years. Cluster analysis based on RFLP banding patterns showed five groupings at 85% similarity. The majority of strains from a given race were contained within one cluster, except for race 3 strains, which were distributed in three of the five clusters.

DNA, Bacterial↗
PubMed2006

Identification, prevalence and population structure of non-typable Streptococcus pneumoniae in carriage samples isolated from preschoolers attending day-care centres.

The authors aimed to get insights into the population structure of non-(sero)typable pneumococci (NTPn), a specific group of natural atypical pneumococci whose identification is often difficult, and which has remained insufficiently studied. A total of 265 presumptive NTPn, isolated between 1997 and 2003 from the nasopharynx of children, were characterized. Strains were confirmed to be pneumococci on the basis of bile solubility, and PCR detection or Southern blotting hybridization of lytA and psaA, genes ubiquitous in this species. Multilocus sequence typing (MLST) was used to exclude two isolates that gave ambiguous results. Non-typability was confirmed by the Quellung reaction using Omniserum. A total of 213 isolates were considered to be true NTPn. The molecular analysis of the true NTPn by PFGE and MLST showed that this population was genetically diverse, although a dominant cluster, accounting for 66 % of the isolates, was identified. Antimicrobial resistance was observed in most genetic backgrounds, and multidrug resistance to penicillin, erythromycin, clindamycin, tetracycline and sulfamethoxazole-trimethoprim was associated with strains belonging to the dominant cluster. Comparison with PFGE fingerprints and sequence types of large collections of serotypable strains showed that the genetic backgrounds of all but two NTPn were different from those found in serotypable strains. In addition, we found that NTPn strains with similar genetic backgrounds to those identified in our study had been isolated from disease sources in other countries. These observations seem to indicate that NTPn have diverse genetic backgrounds and may have evolved as a distinct group of pneumococcal isolates.

Anti-Bacterial Agents↗
PubMed2006

Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus.

The Cape hake species, Merluccius capensis and Merluccius paradoxus are the most important resource of the South African and Namibian demersal fishery, but it is unclear whether there is a single population of each shared by both countries. We analysed the population structure and evolutionary history of these two species using the variable 5' region of the mtDNA control region for 311 specimens of M. capensis and 333 specimens of M. paradoxus sampled between Lüderitz (southern Namibia) to south of Cape Point (South Africa). 107 haplotypes for M. capensis and eight haplotypes for M. paradoxus were recovered. AMOVA and pairwise Phi(st) analyses revealed no structure in M. capensis, however significant genetic differentiation between Namibian and South African 'populations' was detected for M. paradoxus. This was only restricted to mature fish older than 3 and 4 years and not for juvenile fish younger than 3 years. Analyses reveal that M. capensis has undergone population expansion (Fu's Fs=-26.65, P<0.001), possibly within the last 4500-23,000 years, whereas M. paradoxus has not. Our study highlights the utility of genetic markers to unravel the evolutionary history of sympatric species, as well as addressing management issues within regions where commercially valuable fish stocks are shared between nations.

Animals↗
PubMed2004

Combining paternally and maternally inherited mitochondrial DNA for analysis of population structure in mussels.

Sequence divergence for a fragment of the 16S rRNA gene was compared to identify the advantages in using mitochondrial genes that descend separately through the female and male lineages to examine population structure. The test compared divergence among four local species of freshwater mussels (Unionidae) and was extended to multiple populations of one species, Pyganodon grandis. For the same gene, the male-inherited sequences diverged at a faster rate, producing longer branch lengths in the phylogenies. Of particular use were sequences extracted from P. grandis populations from the southern region of the Lake Erie watershed (Ohio, USA); five male-inherited haplotypes were found. Only one change was observed in the female-inherited form in this region. Therefore, more rapid evolution has occurred in the male form of the gene, and this form provided stronger evidence of geographical isolation among populations. A combination of analyses on haplotypes derived through males and females creates complementary opportunities to identify evolutionary relationships caused by drift and migration in mussels.

Animals↗